While Illusion of Gaia features a large cast of characters, Will, Freedan, and Shadow are the only playable characters in the game. Each possesses unique abilities, and certain areas are inaccessible without a specific character. The characters acquire new techniques as part of the story progression. Will's techniques primarily focus on accessing new areas with incidental combat applications, while Freedan's techniques are more combat-oriented. Shadow joins the party later in the game.
Combat is relatively straightforward. Characters share the same health and defense scores but have varying levels of strength. Freedan inflicts more damage than Will and has a longer reach, while Shadow deals more damage than Freedan. Attacks are primarily melee-based, utilizing Will's flute, Freedan's sword, or Shadow's pseudopod. Enemies' health bars are displayed upon attacking, appearing as a series of red spheres that represent hit points. Bosses cannot be revisited, and enemies reappear only when Will loses all his lives or exits an area and returns.